Transcription factor IIH, or TFIIH, pronounced “TF two H,” is a true workhorse among the protein complexes that control human cell activity. It plays critical roles in transcription—the highly regulated enzymatic synthesis of RNA from a DNA template—and in the repair of damaged DNA. But how can a single protein assembly participate in two very different and extremely important genomic tasks?
A team of researchers led by chemistry professor Ivaylo Ivanov at Georgia State University used the Summit supercomputer at the Department of Energy’s Oak Ridge National Laboratory to help answer that question. By conducting several molecular dynamics simulations of TFIIH in the transcription and DNA repair-competent states and then comparing the structural mechanisms at work, Ivanov and his team made an interesting discovery: TFIIH is a shapeshifter, reconfiguring itself to meet the demands of each task.
Unraveling the inner workings of TFIIH at the interface of transcription and DNA repair is key for understanding the origins of genetic disorders caused by mutations—inherited diseases such as xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome. The GSU team published its results in the journal Communication in Nature.
“This project illustrates how versatile protein assemblies are, because they are involved in so many cellular processes. Understanding how genetic mutations impair the function of TFIIH is the first step in designing of treatment strategies such as gene editing,” Ivanov said.
The project’s findings are just the latest in Ivanov’s ongoing research into the molecular machinery of gene expression using supercomputers at the Oak Ridge Leadership Computing Facility, a DOE Office of Science user facility at ORNL.
Transcription initiation versus DNA repair
The structure of TFIIH was mapped by cryo-electron microscopy, but understanding its functional dynamics during transcription initiation and DNA repair required the GSU team to model the large-scale dynamics of systems of nearly 2 million atoms—with multiple copies. which run simultaneously.
“We often rely on chain-of-replication simulations to describe large-scale conformational changes in biomolecular complexes,” Ivanov said. “To perform these types of simulations, you must be able to run multiple replicas of the simulation system at the same time. This is only possible if you have multiple GPU nodes available, such as Summit. In one case, using we have about 70 replicas, so the computational cost of delineating any of these mechanisms quickly increases.”
TFIIH is an integral part of the transcription preinitiation complex, or PIC, which is an assembly of proteins important in gene expression that Ivanov and his team at Summit also modeled. As its name suggests, PIC helps trigger the transcription process where the DNA sequence of a gene is copied into messenger RNA. The mRNA then delivers that genetic information to the cytoplasm of the cell, where it is translated into a protein, thus allowing it to begin its encoded function, for example, preventing disease or providing energy.
“TFIIH is part of the assembly that contains the molecular motor that removes the duplex DNA at a specific location in the genome and pushes it towards the RNA polymerase active site. will not work,” said Ivanov.
Transcription factor IIH is also a key component of the protein machinery that facilitates nucleotide excision repair—a versatile DNA repair pathway that removes a wide range of genomic lesions resulting from factors such as in ultraviolet light, chemotherapy treatments and exposure to environmental carcinogens.
The team pointed out how the two subunits of TFIIH, XPB and XPD, act differently to modify DNA. XPB and XPD sit on the edges of the horseshoe-shaped TFIIH assembly. At the start of transcription, the horseshoe has an open conformation in XPB that serves as the active component that removes DNA. XPD, on the other hand, fulfills a purely structural role—DNA is directed away from it, and its DNA binding groove is blocked.
“XPD is regulated in a way to prevent it from processing DNA. Another subunit of TFIIH called p62 serves a regulatory role—it inserts itself into the DNA binding groove of XPD and blocks its function , “said Ivanov.
However, when scanning lesions during DNA repair—either nucleotide excision repair or transcription-coupled NER—TFIIH adopts a closed conformation, and the roles of XPB and XPD reversed.
“Previously, we modeled the TFIIH dynamics inside the PIC, which allowed us to divide the complex into functional modules,” Ivanov said. “We noticed that, interestingly, the interfaces between the functional modules harbored most of the TFIIH mutations associated with the disease. However, at that time, we did not have simulations of the nucleotide excision repair competent state—and that provided an incomplete picture of what TFIIH is doing in DNA repair.”
The new, detailed picture of the mechanistic dynamics of TFIIH provides insights into the key mechanisms that allow TFIIH to modify DNA at transcription initiation versus nucleotide excision repair. This can be useful information in finding treatment for genetic disorders.
“New computational methods, such as those described in this report, revive static images of biological machines and advance dynamic views of how they work,” said Manju Hingorani, a director of the National Science Foundation’s Director of Biological Sciences program. “In this case, new knowledge of how a protein complex changes and regulates itself to allow repair of damaged DNA and restoration of cellular function can explain how defects in the process cause disease.”
Dynamic structural analysis
The GSU team used graph algorithms to divide TFIIH’s protein network into strongly connected components, thereby allowing them to identify dynamic modules—the pieces that work together. In turn, these models show how the modules behave in relation to other parts of the structure.
“Now we can compare and contrast the functional dynamics of TFIIH when it is active in transcription versus when it is active in nucleotide excision repair,” Ivanov said. “All of a sudden, you see communities that were previously locked together start to open up and engage in activities that you wouldn’t expect just by looking at the transcription-competent state.”
Researchers can also map different types of information to the protein network model, such as dynamic correlations or contact probabilities. This allows them to focus on important interfaces that change with each structural transition and analyze them in detail. It may be possible to classify mutations into different disease phenotypes based on where they sit in the TFIIH structure and the dynamic roles they play.
“Having these different dynamic ensembles in the case of transcription versus the competent state of NER, you can do a detailed analysis of how the patient’s mutations for different genetic diseases are positioned in relation to the dynamics community that we know,” Ivanov said. “Basically, there is a possibility—by understanding the mechanisms of transcription and NER of TFIIH—to direct its function to one or the other pathway.”
Jina Yu et al, Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and affects genetic diseases, Communication in Nature (2023). DOI: 10.1038/s41467-023-38416-6
Provided by Oak Ridge National Laboratory
Citation: DNA-repair protein complex is a shapeshifter, reconfiguring itself to meet the demands of each task (2023, July 10) retrieved 11 July 2023 from https://phys.org/news/2023-07 -dna-repair-protein-complex-shapeshifter-reconfiguring.html
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